Bug fix in AtomSelectionPlugin

Slight change in atom selection selectors name

MDANSE/App/GUI/Framework/Plugins/AtomSelectionPlugin.py

@@ -139,12 +139,13 @@ class Query(object):
             return []
                             
         try:
-            selection = self._parser(self.get_expression(),True)
+            expression = self.get_expression()
+            selection = self._parser.parse(expression)
         except AtomSelectionParserError:
-            selection = ("",[])
-
-        return selection       
-                
+            return ("",[])
+        else:
+            return (expression,selection)
+            
     def pop(self):
         return self._list.pop()
     
@@ -178,7 +179,7 @@ class AtomSelectionPlugin(ComponentPlugin):
                                                 
         self._mainPanel = wx.Panel(self, wx.ID_ANY, size=self.GetSize())
 
-        self._notebook = wxaui.AuiNotebook(self._mainPanel, wx.ID_ANY, style=wxaui.AUI_NB_DEFAULT_STYLE^wxaui.AUI_NB_TAB_MOVE)
+        self._notebook = wxaui.AuiNotebook(self._mainPanel, wx.ID_ANY, style=wxaui.AUI_NB_DEFAULT_STYLE&~wxaui.AUI_NB_CLOSE_ON_ACTIVE_TAB&~wxaui.AUI_NB_TAB_MOVE)
         
         settingsPanel = wx.Panel(self._mainPanel,wx.ID_ANY)
                 
@@ -321,7 +322,7 @@ class AtomSelectionPlugin(ComponentPlugin):
         
         self._selectionSummary.AppendText("List of selected atoms:\n")
         for idx in self._selection:
-            self._selectionSummary.AppendText("\t%s\n" % self._atoms[idx].fullName())
+            self._selectionSummary.AppendText("\t%s (MMTK index: %d)\n" % self._atoms[idx].fullName(),self._atoms[idx].index)
 
     def insert_keyword_values(self, keyword, values):
 
@@ -378,7 +379,7 @@ class AtomSelectionPlugin(ComponentPlugin):
             return
                                 
         if not self._selectors.has_key(selectionFilter):
-            self._selectors[selectionFilter] = [str(v) for v in REGISTRY["selector"](selectionFilter, self._parent.trajectory.universe).choices]
+            self._selectors[selectionFilter] = [str(v) for v in REGISTRY["selector"][selectionFilter](self._parent.trajectory.universe).choices]
         
         self.values.Set(self._selectors[selectionFilter])
 

MDANSE/App/GUI/MainFrame.py

@@ -207,6 +207,7 @@ https://github.com/eurydyce/MDANSE/tree/master/MDANSE
 for any other request, please send an email to:
 
 \tpellegrini@ill.fr
+\tgonzalezm@ill.fr
 \tjohnson@ill.fr
 
 or directly to the MDANSE mailing list:

MDANSE/Framework/AtomSelectionParser.py

@@ -41,9 +41,9 @@ class AtomSelectionParserError(Error):
 
 class AtomSelectionParser(object):
         
-    def __init__(self, trajectory):
+    def __init__(self, universe):
         
-        self._universe = trajectory.universe
+        self._universe = universe
                 
     def operator_and(self, token):
         

MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -92,7 +92,7 @@ class AtomSelectionConfigurator(IConfigurator):
             ud = UD_STORE[trajConfig["basename"],"atom_selection",value]        
         # The input value is an atom selection string: parse it and update the configuration
         except UserDefinitionError:
-            parser = AtomSelectionParser(trajConfig["instance"])
+            parser = AtomSelectionParser(trajConfig["instance"].universe)
             self["indexes"] = parser.parse(value)
             self["expression"] = value
         else:

MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -89,7 +89,7 @@ class AtomTransmutationConfigurator(IConfigurator):
 
         trajConfig = configuration[self._dependencies['trajectory']]
                                                                 
-        parser = AtomSelectionParser(trajConfig["instance"])
+        parser = AtomSelectionParser(trajConfig["instance"].universe)
         
         # If the input value is a dictionary, it must have a selection string as key and the element 
         # to be transmutated to as value 

MDANSE/Framework/Jobs/Converters/DMol.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Jun 4, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+from MDANSE.Framework.Jobs.Converters.Discover import DiscoverConverter
+        
+class DMolConverter(DiscoverConverter):
+    """
+    Converts a DMol trajectory to a MMTK trajectory.
+    """
+
+    type = 'dmol'
+    
+    label = "DMol"
\ No newline at end of file

MDANSE/Framework/Selectors/AtomFullName.py

@@ -34,12 +34,12 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
                 
 class AtomFullName(ISelector):
 
-    type = "atomfullname"
+    type = "atom_fullname"
 
     section = "atoms"
 
     def __init__(self, universe):
-
+        
         ISelector.__init__(self,universe)
                 
         self._choices.extend(sorted(set([at.fullName().strip().lower() for at in self._universe.atomList()])))

MDANSE/Framework/Selectors/AtomIndex.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class AtomIndex(ISelector):
 
-    type = "atomindex"
+    type = "atom_index"
 
     section = "atoms"
 

MDANSE/Framework/Selectors/AtomName.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class AtomName(ISelector):
 
-    type = "atomname"
+    type = "atom_name"
 
     section = "atoms"
 

MDANSE/Framework/Selectors/AtomPicked.py

@@ -34,6 +34,6 @@ from MDANSE.Framework.Selectors.AtomIndex import AtomIndex
         
 class AtomPicked(AtomIndex):
 
-    type = "atompicked"
+    type = "atom_picked"
 
     section = "miscellaneous"

MDANSE/Framework/Selectors/AtomSymbol.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class AtomSymbol(ISelector):
 
-    type = "atomsymbol"
+    type = "atom_symbol"
 
     section = "atoms"
 

MDANSE/Framework/Selectors/AtomType.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class AtomType(ISelector):
 
-    type = "atomtype"
+    type = "atom_type"
 
     section = "atoms"
 

MDANSE/Framework/Selectors/CarboHydrogen.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
     
 class CarboHydrogen(ISelector):
     
-    type = "carbohydrogen"
+    type = "carbo_hydrogen"
     
     section = "hydrogens"
 

MDANSE/Framework/Selectors/ChainName.py

@@ -36,7 +36,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class ChainName(ISelector):
 
-    type = "chainname"
+    type = "chain_name"
 
     section = "proteins"
 

MDANSE/Framework/Selectors/HeteroHydrogen.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class HeteroHydrogenBound(ISelector):
     
-    type = "heterohydrogen"
+    type = "hetero_hydrogen"
     
     section = "hydrogens"
 

MDANSE/Framework/Selectors/MoleculeIndex.py

@@ -27,7 +27,7 @@
 ''' 
 Created on Mar 27, 2015
 
-@author: pellegrini
+:author: Eric C. Pellegrini
 '''
 
 from MDANSE.Framework.Selectors.ISelector import ISelector

MDANSE/Framework/Selectors/NitroHydrogen.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class NitroHydrogen(ISelector):
     
-    type = "nitrohydrogen"
+    type = "nitro_hydrogen"
     
     section = "hydrogens"
 

MDANSE/Framework/Selectors/OxyHydrogen.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
 
 class OxyHydrogen(ISelector):
     
-    type = "O-H"
+    type = "oxy_hydrogen"
     
     section = "hydrogens"
 

MDANSE/Framework/Selectors/PythonScript.py

@@ -34,7 +34,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
                 
 class PythonScript(ISelector):
     
-    type = "pythonscript"
+    type = "python_script"
     
     section = None
 

MDANSE/Framework/Selectors/ResidueType.py

@@ -36,7 +36,7 @@ from MDANSE.Framework.Selectors.ISelector import ISelector
         
 class ResType(ISelector):
 
-    type = "restype"
+    type = "residue_type"
 
     section = "proteins"
 

Tests/UnitTests/TestConfigurator.py

@@ -265,7 +265,7 @@ class TestConfigurator(UnitTest):
   
         # Test a valid atom selection string
         self._parameters["trajectory"] = self._validTrajectory.filename
-        self._parameters["atom_selection"] = 'atomtype carbon'
+        self._parameters["atom_selection"] = 'atom_type carbon'
         self.assertNotRaises(configurable.setup,self._parameters)
         self.assertEqual(configurable['atom_selection']['n_selected_atoms'],sum([True for at in configurable['trajectory']['instance'].universe.atomList() if at.symbol=='C']))
   
@@ -291,7 +291,7 @@ class TestConfigurator(UnitTest):
   
         # Test that an empty selection selection raises a SelectionParserError
         self._parameters["trajectory"] = self._validTrajectory.filename
-        self._parameters["atom_transmutation"] = 'atomtype(["fsfsd"])'
+        self._parameters["atom_transmutation"] = 'atom_type(["fsfsd"])'
         self.assertRaises(ConfiguratorError,configurable.setup,self._parameters)
   
         # Test that None parameters selects everything